Variant report

Variant	rs9938177
Chromosome Location	chr16:31278991-31278992
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr16:31278656-31279104	MCF10A-Er-Src	breast:	n/a	n/a
2	MYC	chr16:31278642-31279017	MCF10A-Er-Src	breast:	n/a	n/a
3	JUN	chr16:31278403-31279138	K562	blood:	n/a	chr16:31278859-31278869 chr16:31278861-31278872 chr16:31278859-31278869 chr16:31278859-31278869
4	FOS	chr16:31278661-31279049	MCF10A-Er-Src	breast:	n/a	chr16:31278859-31278869 chr16:31278861-31278872 chr16:31278859-31278869 chr16:31278859-31278869
5	JUND	chr16:31278724-31278999	H1-hESC	embryonic stem cell:	n/a	chr16:31278858-31278869 chr16:31278859-31278869 chr16:31278861-31278872 chr16:31278859-31278869 chr16:31278859-31278869
6	STAT3	chr16:31278629-31279044	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr16:31278710-31279054	MCF10A-Er-Src	breast:	n/a	chr16:31278859-31278869 chr16:31278861-31278872 chr16:31278859-31278869 chr16:31278859-31278869
8	STAT3	chr16:31278647-31279044	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr16:31278690-31278994	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr16:31278639-31279075	MCF10A-Er-Src	breast:	n/a	chr16:31278859-31278869 chr16:31278861-31278872 chr16:31278859-31278869 chr16:31278859-31278869
11	JUND	chr16:31278732-31279016	K562	blood:	n/a	chr16:31278858-31278869 chr16:31278859-31278869 chr16:31278861-31278872 chr16:31278859-31278869 chr16:31278859-31278869

No.	Distal block	Cell Line	Cell type
1	chr16:31278411..31282963-chr16:31285984..31289052,5	MCF-7	breast:
2	chr16:31225508..31229530-chr16:31277117..31281279,6	MCF-7	breast:
3	chr16:31225327..31230953-chr16:31277531..31282411,8	MCF-7	breast:
4	chr16:31272641..31274677-chr16:31278876..31282230,3	MCF-7	breast:
5	chr16:31273033..31275008-chr16:31278904..31280780,2	K562	blood:
6	chr16:31278987..31281601-chr16:31282208..31284163,2	MCF-7	breast:

Variant related genes	Relation type
ITGAM	TF binding region
RNU7-199P	TF binding region
ENSG00000177238	Chromatin interaction
ENSG00000169900	Chromatin interaction
ENSG00000169896	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10438639	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11641624	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11645526	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11863627	0.81[EUR][1000 genomes]
rs11865830	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1808430	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2011491	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2359661	0.84[ASN][1000 genomes]
rs3087796	0.80[EUR][1000 genomes]
rs3764327	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3815801	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4447446	0.84[ASN][1000 genomes]
rs4561481	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4597342	0.80[EUR][1000 genomes]
rs4889639	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4889640	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4889644	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60660286	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6565225	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7193943	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7196256	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7499192	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8044075	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8047985	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8048583	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8051304	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8057320	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8062426	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs889549	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs889551	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs929868	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9923270	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431451	chr16:30682399-31340999	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9938177	PYDC1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31276600-31279600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr16:31277200-31279200	Enhancers	NHEK	skin
3	chr16:31277200-31279400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr16:31277200-31283200	Weak transcription	Lung	lung
5	chr16:31277400-31284600	Weak transcription	HMEC	breast
6	chr16:31277400-31289000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr16:31277400-31290000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr16:31277600-31279000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr16:31277600-31279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr16:31277600-31279200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr16:31277600-31283200	Weak transcription	Spleen	Spleen
12	chr16:31277600-31284800	Weak transcription	Primary B cells from cord blood	blood
13	chr16:31277600-31285000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr16:31277600-31290400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr16:31277600-31290400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr16:31277600-31290600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr16:31277800-31279200	Weak transcription	GM12878-XiMat	blood
18	chr16:31277800-31284800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:31278000-31286600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr16:31278400-31279200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr16:31278400-31279400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr16:31278400-31279400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr16:31278400-31279600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr16:31278600-31279000	Enhancers	A549	lung
25	chr16:31278600-31279400	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr16:31278600-31280200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr16:31278800-31279200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:31278800-31279200	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr16:31278800-31279400	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr16:31278800-31279400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr16:31278800-31279600	Enhancers	H9 Cell Line	embryonic stem cell
32	chr16:31278800-31279800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr16:31278800-31280000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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